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Yorodumi- PDB-1ckp: HUMAN CYCLIN DEPENDENT KINASE 2 COMPLEXED WITH THE INHIBITOR PURV... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ckp | ||||||
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Title | HUMAN CYCLIN DEPENDENT KINASE 2 COMPLEXED WITH THE INHIBITOR PURVALANOL B | ||||||
Components | PROTEIN (CYCLIN-DEPENDENT PROTEIN KINASE 2) | ||||||
Keywords | HORMONE/GROWTH FACTOR / PROTEIN KINASE / CELL CYCLE / PHOSPHORYLATION / CELL DIVISION / MITOSIS / INHIBITION / HORMONE-GROWTH FACTOR COMPLEX | ||||||
Function / homology | Function and homology information Replication initiator protein RctB, central region / RctB, helix turn helix domain / Vibrionales, replication initiator protein RctB, central region / RctB helix turn helix domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / 2-Layer Sandwich ...Replication initiator protein RctB, central region / RctB, helix turn helix domain / Vibrionales, replication initiator protein RctB, central region / RctB helix turn helix domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 2.05 Å | ||||||
Authors | Gray, N.S. / Thunnissen, A.M.W.H. / Schultz, P.G. / Kim, S.H. | ||||||
Citation | Journal: Science / Year: 1998 Title: Exploiting chemical libraries, structure, and genomics in the search for kinase inhibitors. Authors: Gray, N.S. / Wodicka, L. / Thunnissen, A.M. / Norman, T.C. / Kwon, S. / Espinoza, F.H. / Morgan, D.O. / Barnes, G. / LeClerc, S. / Meijer, L. / Kim, S.H. / Lockhart, D.J. / Schultz, P.G. #1: Journal: Eur.J.Biochem. / Year: 1997 Title: Inhibition of Cyclin-Dependent Kinases by Purine Analogues-Crystal Structure of Human Cdk2 Complexed with Roscovitine Authors: De Azevedo, W.F. / Leclerc, S. / Meijer, L. / Havlicek, L. / Strnad, M. / Kim, S.H. #2: Journal: Protein Sci. / Year: 1995 Title: Multiple Modes of Ligand Recognition: Crystal Structures of Cyclin-Dependent Protein Kinase 2 in Complex with ATP and Two Inhibitors, Olomoucine and Isopentenyladenine Authors: Schultze-Gahmen, U. / Brandsen, J. / Jones, H.D. / Morgan, D.O. / Meijer, L. / Vesely, J. / Kim, S.H. #3: Journal: Nature / Year: 1993 Title: Crystal Structure of Cyclin-Dependent Kinase 2 Authors: De Bondt, H.L. / Rosenblatt, J. / Jancarik, J. / Jones, H.D. / Morgan, D.O. / Kim, S.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ckp.cif.gz | 72.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ckp.ent.gz | 53 KB | Display | PDB format |
PDBx/mmJSON format | 1ckp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ckp_validation.pdf.gz | 491.5 KB | Display | wwPDB validaton report |
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Full document | 1ckp_full_validation.pdf.gz | 493.2 KB | Display | |
Data in XML | 1ckp_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | 1ckp_validation.cif.gz | 11.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/1ckp ftp://data.pdbj.org/pub/pdb/validation_reports/ck/1ckp | HTTPS FTP |
-Related structure data
Related structure data | 1hckS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33976.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: SF9 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P24941, EC: 2.7.1.37 |
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#2: Chemical | ChemComp-PVB / |
#3: Chemical | ChemComp-EDO / |
#4: Water | ChemComp-HOH / |
Nonpolymer details | 3-CHLORO-4-CARBOXYANI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 36 % |
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Crystal grow | pH: 7.4 / Details: pH 7.4 |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Feb 15, 1996 / Details: MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→32 Å / Num. obs: 17655 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.05→2.11 Å / Rmerge(I) obs: 0.185 / % possible all: 91.6 |
Reflection shell | *PLUS % possible obs: 91.6 % |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: PDB ENTRY 1HCK Resolution: 2.05→32 Å / Isotropic thermal model: RESTRAINED / Cross valid method: FREE-R / σ(F): 2 Details: REFINEMENT BEGUN WITH X-PLOR PC AND RIGID BODY REFINEMENT. ETHYLENE GLYCOL MOLECULE HAS BEEN REFINED WITH OCCUPANCY OF 0.7
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Displacement parameters | Biso mean: 30.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.05→32 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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